Create figures for CyTOF myeloid panel data. Preprocessing and preliminary analysis were done by Dimitrios N. Sidiropoulos.

Cell proportions

Bar plot

## 
## Baseline     C1D1     C2D1 
##       28       28        8
## The number of paired samples between Baseline and C1D1: 28 
## The number of paired samples between Baseline and C2D1: 8 
## The number of paired samples between C2D1 and C1D1: 8

Table

P-values from paired two-sided Wilcoxon test between time points and mean of difference between time points

pValue_BvsC1D1 mean(C1D1-B) pValue_C1D1vsC2D1 mean(C2D1-C1D1) pValue_BvsC2D2 mean(C2D1-B)
B 0.000 -1.399 0.023 -1.174 0.008 -2.674
cDC1 0.479 -0.078 0.109 0.712 0.250 0.894
cDC2 0.000 -0.263 0.844 -0.059 0.109 -0.436
DNT 0.008 -0.247 0.547 -0.157 0.109 -0.235
Early Myelocyte 0.001 -1.085 0.844 0.703 0.383 -0.112
Granulocytes 0.937 -0.006 0.109 -0.007 0.078 -0.004
Non-Classical Mono 0.264 -0.394 0.844 0.746 0.742 -0.324
pDC 0.000 -0.461 0.547 0.122 0.547 -0.152
preDC/Classical Mono 0.007 8.032 0.313 6.048 0.016 16.117
Tc 0.662 -0.525 0.023 -2.823 0.008 -2.930
Th 0.090 -3.574 0.250 -4.110 0.008 -10.144 
## [1] "Significant change (p-value < 0.05) in proportions of cells in the following cell types:"
## $pValue_BvsC1D1
## [1] "B"                    "cDC2"                 "DNT"                 
## [4] "Early Myelocyte"      "pDC"                  "preDC/Classical Mono"
## 
## $pValue_C1D1vsC2D1
## [1] "B"  "Tc"
## 
## $pValue_BvsC2D2
## [1] "B"                    "preDC/Classical Mono" "Tc"                  
## [4] "Th"

Boxplots

For significant cell types only

Average expression of markers by cluster

Table

Boxplots

two time points

## [1] "The number of pairs (cluster, marker) with significant change (p-value < 0.05) in marker expression between baseline and C1D1:"
## [1] 152
## [1] "CD19 in B"

## [1] "CD117 in B"

## [1] "CD11B in B"

## [1] "CD1C in B"

## [1] "CCR2 in B"

## [1] "CD123 in B"

## [1] "CLEC9A in B"

## [1] "CD11C in B"

## [1] "CD141 in B"

## [1] "CD80 in B"

## [1] "TLR4 in B"

## [1] "CD172AB in B"

## [1] "CD40 in B"

## [1] "CD206 in B"

## [1] "HLADR in B"

## [1] "CD68 in B"

## [1] "PDL1 in B"

## [1] "CD3 in cDC1"

## [1] "CD11B in cDC1"

## [1] "CD4 in cDC1"

## [1] "CD8 in cDC1"

## [1] "CXCR2 in cDC1"

## [1] "CD1C in cDC1"

## [1] "FCERI in cDC1"

## [1] "CCR5 in cDC1"

## [1] "CLEC9A in cDC1"

## [1] "CD11C in cDC1"

## [1] "TLR4 in cDC1"

## [1] "CD40 in cDC1"

## [1] "CD206 in cDC1"

## [1] "CD33 in cDC1"

## [1] "CD68 in cDC1"

## [1] "CD116 in cDC1"

## [1] "PDL1 in cDC1"

## [1] "CD135 in cDC1"

## [1] "CD117 in cDC2"

## [1] "CD11B in cDC2"

## [1] "CD4 in cDC2"

## [1] "CD14 in cDC2"

## [1] "FCERI in cDC2"

## [1] "CD103 in cDC2"

## [1] "CCR2 in cDC2"

## [1] "CD123 in cDC2"

## [1] "CCR5 in cDC2"

## [1] "CD11C in cDC2"

## [1] "TLR4 in cDC2"

## [1] "CD172AB in cDC2"

## [1] "CD40 in cDC2"

## [1] "PDL2 in cDC2"

## [1] "CCR7 in cDC2"

## [1] "CD206 in cDC2"

## [1] "HLADR in cDC2"

## [1] "CD68 in cDC2"

## [1] "CD15 in cDC2"

## [1] "PDL1 in cDC2"

## [1] "CD16 in cDC2"

## [1] "Arg1 in cDC2"

## [1] "CD8 in DNT"

## [1] "CD163 in DNT"

## [1] "CLEC9A in DNT"

## [1] "CD11C in DNT"

## [1] "CD172AB in DNT"

## [1] "PDL2 in DNT"

## [1] "CCR7 in DNT"

## [1] "HLADR in DNT"

## [1] "PDL1 in DNT"

## [1] "CD3 in Early Myelocyte"

## [1] "CD4 in Early Myelocyte"

## [1] "CD8 in Early Myelocyte"

## [1] "CXCR2 in Early Myelocyte"

## [1] "CD66B in Early Myelocyte"

## [1] "CCR2 in Early Myelocyte"

## [1] "CCR5 in Early Myelocyte"

## [1] "CD11C in Early Myelocyte"

## [1] "CD141 in Early Myelocyte"

## [1] "CD40 in Early Myelocyte"

## [1] "PDL1 in Early Myelocyte"

## [1] "CD135 in Early Myelocyte"

## [1] "CD16 in Early Myelocyte"

## [1] "CCR5 in Granulocytes"

## [1] "CXCR4 in Granulocytes"

## [1] "CD4 in Non-Classical Mono"

## [1] "CD8 in Non-Classical Mono"

## [1] "CD14 in Non-Classical Mono"

## [1] "CD1C in Non-Classical Mono"

## [1] "FCERI in Non-Classical Mono"

## [1] "CCR2 in Non-Classical Mono"

## [1] "CD123 in Non-Classical Mono"

## [1] "CCR5 in Non-Classical Mono"

## [1] "CLEC9A in Non-Classical Mono"

## [1] "CD11C in Non-Classical Mono"

## [1] "CD141 in Non-Classical Mono"

## [1] "CD80 in Non-Classical Mono"

## [1] "CCR7 in Non-Classical Mono"

## [1] "CD33 in Non-Classical Mono"

## [1] "CD68 in Non-Classical Mono"

## [1] "CD116 in Non-Classical Mono"

## [1] "PDL1 in Non-Classical Mono"

## [1] "CD135 in Non-Classical Mono"

## [1] "CD16 in Non-Classical Mono"

## [1] "Arg1 in Non-Classical Mono"

## [1] "CD19 in pDC"

## [1] "CD4 in pDC"

## [1] "CCR2 in pDC"

## [1] "CD123 in pDC"

## [1] "TLR4 in pDC"

## [1] "CD172AB in pDC"

## [1] "CD40 in pDC"

## [1] "CD206 in pDC"

## [1] "CD33 in pDC"

## [1] "CD16 in pDC"

## [1] "CD19 in preDC/Classical Mono"

## [1] "CD117 in preDC/Classical Mono"

## [1] "CD11B in preDC/Classical Mono"

## [1] "CD14 in preDC/Classical Mono"

## [1] "CD66B in preDC/Classical Mono"

## [1] "CCR5 in preDC/Classical Mono"

## [1] "CD11C in preDC/Classical Mono"

## [1] "TLR4 in preDC/Classical Mono"

## [1] "CD172AB in preDC/Classical Mono"

## [1] "CD40 in preDC/Classical Mono"

## [1] "PDL2 in preDC/Classical Mono"

## [1] "CD206 in preDC/Classical Mono"

## [1] "PDL1 in preDC/Classical Mono"

## [1] "Arg1 in preDC/Classical Mono"

## [1] "CD1C in Tc"

## [1] "CCR2 in Tc"

## [1] "CD123 in Tc"

## [1] "CCR5 in Tc"

## [1] "CD11C in Tc"

## [1] "CD80 in Tc"

## [1] "CD172AB in Tc"

## [1] "CD33 in Tc"

## [1] "HLADR in Tc"

## [1] "CD68 in Tc"

## [1] "CD15 in Tc"

## [1] "PDL1 in Tc"

## [1] "Arg1 in Tc"

## [1] "CD1C in Th"

## [1] "FCERI in Th"

## [1] "CCR2 in Th"

## [1] "CD123 in Th"

## [1] "CCR5 in Th"

## [1] "CD11C in Th"

## [1] "CD172AB in Th"

## [1] "CD33 in Th"

## [1] "HLADR in Th"

## [1] "CD15 in Th"

## [1] "CXCR4 in Th"

## [1] "CD116 in Th"

## [1] "PDL1 in Th"

## [1] "Arg1 in Th"

three time points

## [1] "CD19 in B"

## [1] "CD117 in B"

## [1] "CD11B in B"

## [1] "CD1C in B"

## [1] "CCR2 in B"

## [1] "CD123 in B"

## [1] "CLEC9A in B"

## [1] "CD11C in B"

## [1] "CD141 in B"

## [1] "CD80 in B"

## [1] "TLR4 in B"

## [1] "CD172AB in B"

## [1] "CD40 in B"

## [1] "CD206 in B"

## [1] "HLADR in B"

## [1] "CD68 in B"

## [1] "PDL1 in B"

## [1] "CD3 in cDC1"

## [1] "CD11B in cDC1"

## [1] "CD4 in cDC1"

## [1] "CD8 in cDC1"

## [1] "CXCR2 in cDC1"

## [1] "CD1C in cDC1"

## [1] "FCERI in cDC1"

## [1] "CCR5 in cDC1"

## [1] "CLEC9A in cDC1"

## [1] "CD11C in cDC1"

## [1] "TLR4 in cDC1"

## [1] "CD40 in cDC1"

## [1] "CD206 in cDC1"

## [1] "CD33 in cDC1"

## [1] "CD68 in cDC1"

## [1] "CD116 in cDC1"

## [1] "PDL1 in cDC1"

## [1] "CD135 in cDC1"

## [1] "CD117 in cDC2"

## [1] "CD11B in cDC2"

## [1] "CD4 in cDC2"

## [1] "CD14 in cDC2"

## [1] "FCERI in cDC2"

## [1] "CD103 in cDC2"

## [1] "CCR2 in cDC2"

## [1] "CD123 in cDC2"

## [1] "CCR5 in cDC2"

## [1] "CD11C in cDC2"

## [1] "TLR4 in cDC2"

## [1] "CD172AB in cDC2"

## [1] "CD40 in cDC2"

## [1] "PDL2 in cDC2"

## [1] "CCR7 in cDC2"

## [1] "CD206 in cDC2"

## [1] "HLADR in cDC2"

## [1] "CD68 in cDC2"

## [1] "CD15 in cDC2"

## [1] "PDL1 in cDC2"

## [1] "CD16 in cDC2"

## [1] "Arg1 in cDC2"

## [1] "CD8 in DNT"

## [1] "CD163 in DNT"

## [1] "CLEC9A in DNT"

## [1] "CD11C in DNT"

## [1] "CD172AB in DNT"

## [1] "PDL2 in DNT"

## [1] "CCR7 in DNT"

## [1] "HLADR in DNT"

## [1] "PDL1 in DNT"

## [1] "CD3 in Early Myelocyte"

## [1] "CD4 in Early Myelocyte"

## [1] "CD8 in Early Myelocyte"

## [1] "CXCR2 in Early Myelocyte"

## [1] "CD66B in Early Myelocyte"

## [1] "CCR2 in Early Myelocyte"

## [1] "CCR5 in Early Myelocyte"

## [1] "CD11C in Early Myelocyte"

## [1] "CD141 in Early Myelocyte"

## [1] "CD40 in Early Myelocyte"

## [1] "PDL1 in Early Myelocyte"

## [1] "CD135 in Early Myelocyte"

## [1] "CD16 in Early Myelocyte"

## [1] "CCR5 in Granulocytes"

## [1] "CXCR4 in Granulocytes"

## [1] "CD4 in Non-Classical Mono"

## [1] "CD8 in Non-Classical Mono"

## [1] "CD14 in Non-Classical Mono"

## [1] "CD1C in Non-Classical Mono"

## [1] "FCERI in Non-Classical Mono"

## [1] "CCR2 in Non-Classical Mono"

## [1] "CD123 in Non-Classical Mono"

## [1] "CCR5 in Non-Classical Mono"

## [1] "CLEC9A in Non-Classical Mono"

## [1] "CD11C in Non-Classical Mono"

## [1] "CD141 in Non-Classical Mono"

## [1] "CD80 in Non-Classical Mono"

## [1] "CCR7 in Non-Classical Mono"

## [1] "CD33 in Non-Classical Mono"

## [1] "CD68 in Non-Classical Mono"

## [1] "CD116 in Non-Classical Mono"

## [1] "PDL1 in Non-Classical Mono"

## [1] "CD135 in Non-Classical Mono"

## [1] "CD16 in Non-Classical Mono"

## [1] "Arg1 in Non-Classical Mono"

## [1] "CD19 in pDC"

## [1] "CD4 in pDC"

## [1] "CCR2 in pDC"

## [1] "CD123 in pDC"

## [1] "TLR4 in pDC"

## [1] "CD172AB in pDC"

## [1] "CD40 in pDC"

## [1] "CD206 in pDC"

## [1] "CD33 in pDC"

## [1] "CD16 in pDC"

## [1] "CD19 in preDC/Classical Mono"

## [1] "CD117 in preDC/Classical Mono"

## [1] "CD11B in preDC/Classical Mono"

## [1] "CD14 in preDC/Classical Mono"

## [1] "CD66B in preDC/Classical Mono"

## [1] "CCR5 in preDC/Classical Mono"

## [1] "CD11C in preDC/Classical Mono"

## [1] "TLR4 in preDC/Classical Mono"

## [1] "CD172AB in preDC/Classical Mono"

## [1] "CD40 in preDC/Classical Mono"

## [1] "PDL2 in preDC/Classical Mono"

## [1] "CD206 in preDC/Classical Mono"

## [1] "PDL1 in preDC/Classical Mono"

## [1] "Arg1 in preDC/Classical Mono"

## [1] "CD1C in Tc"

## [1] "CCR2 in Tc"

## [1] "CD123 in Tc"

## [1] "CCR5 in Tc"

## [1] "CD11C in Tc"

## [1] "CD80 in Tc"

## [1] "CD172AB in Tc"

## [1] "CD33 in Tc"

## [1] "HLADR in Tc"

## [1] "CD68 in Tc"

## [1] "CD15 in Tc"

## [1] "PDL1 in Tc"

## [1] "Arg1 in Tc"

## [1] "CD1C in Th"

## [1] "FCERI in Th"

## [1] "CCR2 in Th"

## [1] "CD123 in Th"

## [1] "CCR5 in Th"

## [1] "CD11C in Th"

## [1] "CD172AB in Th"

## [1] "CD33 in Th"

## [1] "HLADR in Th"

## [1] "CD15 in Th"

## [1] "CXCR4 in Th"

## [1] "CD116 in Th"

## [1] "PDL1 in Th"

## [1] "Arg1 in Th"

## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8 
## [2] LC_CTYPE=English_United States.utf8   
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] ashr_2.2-63                 pheatmap_1.0.12            
##  [3] scales_1.3.0                Matrix_1.6-3               
##  [5] data.table_1.14.8           BiocManager_1.30.22        
##  [7] survival_3.5-7              binom_1.1-1.1              
##  [9] flextable_0.9.4             survminer_0.4.9            
## [11] msigdbr_7.5.1               fgsea_1.26.0               
## [13] EnhancedVolcano_1.18.0      ComplexHeatmap_2.16.0      
## [15] DESeq2_1.40.2               SummarizedExperiment_1.30.2
## [17] Biobase_2.60.0              MatrixGenerics_1.12.3      
## [19] matrixStats_1.1.0           GenomicRanges_1.52.1       
## [21] GenomeInfoDb_1.36.4         IRanges_2.34.1             
## [23] S4Vectors_0.38.2            BiocGenerics_0.46.0        
## [25] kableExtra_1.3.4            pals_1.8                   
## [27] gridExtra_2.3               DT_0.30                    
## [29] ggrepel_0.9.4               ggpubr_0.6.0               
## [31] ggplot2_3.4.4               dplyr_1.1.2                
## [33] knitr_1.45                 
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.2           later_1.3.1             bitops_1.0-7           
##   [4] tibble_3.2.1            lifecycle_1.0.4         rstatix_0.7.2          
##   [7] mixsqp_0.3-54           doParallel_1.0.17       lattice_0.21-9         
##  [10] crosstalk_1.2.1         backports_1.4.1         magrittr_2.0.3         
##  [13] sass_0.4.8              rmarkdown_2.25          jquerylib_0.1.4        
##  [16] yaml_2.3.7              httpuv_1.6.12           zip_2.3.0              
##  [19] askpass_1.2.0           cowplot_1.1.2           mapproj_1.2.11         
##  [22] RColorBrewer_1.1-3      maps_3.4.1.1            abind_1.4-5            
##  [25] zlibbioc_1.46.0         rvest_1.0.3             purrr_1.0.2            
##  [28] RCurl_1.98-1.13         gdtools_0.3.4           circlize_0.4.15        
##  [31] GenomeInfoDbData_1.2.10 KMsurv_0.1-5            irlba_2.3.5.1          
##  [34] crul_1.4.0              svglite_2.1.2           commonmark_1.9.0       
##  [37] codetools_0.2-19        DelayedArray_0.26.7     ggtext_0.1.2           
##  [40] xml2_1.3.5              tidyselect_1.2.0        shape_1.4.6            
##  [43] httpcode_0.3.0          farver_2.1.1            webshot_0.5.5          
##  [46] jsonlite_1.8.7          GetoptLong_1.0.5        ellipsis_0.3.2         
##  [49] iterators_1.0.14        systemfonts_1.0.5       foreach_1.5.2          
##  [52] tools_4.3.2             ragg_1.2.6              snow_0.4-4             
##  [55] Rcpp_1.0.11             glue_1.6.2              xfun_0.39              
##  [58] withr_2.5.2             fastmap_1.1.1           fansi_1.0.4            
##  [61] openssl_2.1.1           digest_0.6.33           truncnorm_1.0-9        
##  [64] R6_2.5.1                mime_0.12               textshaping_0.3.7      
##  [67] colorspace_2.1-0        dichromat_2.0-0.1       markdown_1.12          
##  [70] utf8_1.2.3              tidyr_1.3.0             generics_0.1.3         
##  [73] fontLiberation_0.1.0    httr_1.4.7              htmlwidgets_1.6.4      
##  [76] S4Arrays_1.0.6          pkgconfig_2.0.3         gtable_0.3.4           
##  [79] XVector_0.40.0          survMisc_0.5.6          htmltools_0.5.7        
##  [82] fontBitstreamVera_0.1.1 carData_3.0-5           clue_0.3-65            
##  [85] png_0.1-8               km.ci_0.5-6             rstudioapi_0.15.0      
##  [88] reshape2_1.4.4          rjson_0.2.21            uuid_1.1-1             
##  [91] curl_5.1.0              zoo_1.8-12              cachem_1.0.8           
##  [94] GlobalOptions_0.1.2     stringr_1.5.1           parallel_4.3.2         
##  [97] pillar_1.9.0            vctrs_0.6.3             promises_1.2.1         
## [100] car_3.1-2               xtable_1.8-4            cluster_2.1.4          
## [103] evaluate_0.23           invgamma_1.1            cli_3.6.1              
## [106] locfit_1.5-9.8          compiler_4.3.2          rlang_1.1.1            
## [109] crayon_1.5.2            SQUAREM_2021.1          ggsignif_0.6.4         
## [112] labeling_0.4.3          plyr_1.8.9              stringi_1.8.1          
## [115] viridisLite_0.4.2       BiocParallel_1.34.2     babelgene_22.9         
## [118] munsell_0.5.0           fontquiver_0.2.1        gfonts_0.2.0           
## [121] shiny_1.8.0             highr_0.10              gridtext_0.1.5         
## [124] broom_1.0.5             bslib_0.6.1             fastmatch_1.1-4        
## [127] officer_0.6.3